tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Math and other minor edits to some fix style doc pages

Browse Source
This commit is contained in:
Karl Hammond
2022-09-01 16:15:18 -05:00
parent c03ef56965
commit af168d5f80
4 changed files with 151 additions and 139 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
doc/src/fix_atc.rst
View File

@ -6,7 +6,7 @@ fix atc command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix <fixID> <group> atc <type> <parameter_file>
@ -40,8 +40,8 @@ This fix is the beginning to creating a coupled FE/MD simulation and/or
an on-the-fly estimation of continuum fields. The coupled versions of
this fix do Verlet integration and the post-processing does not. After
instantiating this fix, several other fix_modify commands will be
needed to set up the problem, e.g. define the finite element mesh and
prescribe initial and boundary conditions.
needed to set up the problem (i.e., define the finite element mesh and
prescribe initial and boundary conditions).
.. image:: JPG/atc_nanotube.jpg
:align: center
@ -135,7 +135,7 @@ fix are listed below.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the energy
discussed in the previous paragraph. The scalar value is "extensive".
discussed in the previous paragraph. The scalar value is "extensive."
No parameter of this fix can be used with the
*start/stop* keywords of the :doc:`run <run>` command. This fix is not
@ -147,7 +147,7 @@ Restrictions
Thermal and two_temperature (coupling) types use a Verlet
time-integration algorithm. The hardy type does not contain its own
time-integrator and must be used with a separate fix that does contain
one, e.g. nve, nvt, etc. In addition, currently:
one (e.g., nve, nvt). In addition, currently:
* the coupling is restricted to thermal physics
* the FE computations are done in serial on each processor.
@ -159,8 +159,8 @@ Related commands
After specifying this fix in your input script, several
:doc:`fix_modify AtC <fix_modify>` commands are used to setup the
problem, e.g. define the finite element mesh and prescribe initial and
boundary conditions. Each of these options has its own doc page.
problem (e.g., define the finite element mesh and prescribe initial and
boundary conditions). Each of these options has its own doc page.
*fix_modify* commands for setup:
@ -311,6 +311,6 @@ and Computation (2011), 7:1736.
as a field variable from molecular dynamics simulations." Journal of
Chemical Physics (2013), 139:054115.
Please refer to the standard finite element (FE) texts, e.g. T.J.R
Hughes " The finite element method ", Dover 2003, for the basics of FE
simulation.
Please refer to the standard finite element (FE) texts (e.g., T.J.R.
Hughes, *The Finite Element Method,* Dover 2003) for the basics of FE
simulations.

19
doc/src/fix_atom_swap.rst
View File

@ -6,7 +6,7 @@ fix atom/swap command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID atom/swap N X seed T keyword values ...
@ -48,7 +48,7 @@ This fix performs Monte Carlo swaps of atoms of one given atom type
with atoms of the other given atom types. The specified T is used in
the Metropolis criterion dictating swap probabilities.
Perform X swaps of atoms of one type with atoms of another type
Perform :math:`X` swaps of atoms of one type with atoms of another type
according to a Monte Carlo probability. Swap candidates must be in the
fix group, must be in the region (if specified), and must be of one of
the listed types. Swaps are attempted between candidates that are
@ -57,7 +57,7 @@ atoms. Swaps are not attempted between atoms of the same type since
nothing would happen.
All atoms in the simulation domain can be moved using regular time
integration displacements, e.g. via :doc:`fix nvt <fix_nh>`, resulting
integration displacements (e.g., via :doc:`fix nvt <fix_nh>`), resulting
in a hybrid MC+MD simulation. A smaller-than-usual timestep size may
be needed when running such a hybrid simulation, especially if the
swapped atoms are not well equilibrated.
@ -83,9 +83,8 @@ canonical ensemble, the composition of the system can change. Note
that when using *semi-grand*, atoms in the fix group whose type is not
listed in the *types* keyword are ineligible for attempted
conversion. An attempt is made to switch the selected atom (if
eligible) to one of the other listed types with equal
probability. Acceptance of each attempt depends upon the Metropolis
criterion.
eligible) to one of the other listed types with equal probability.
Acceptance of each attempt depends upon the Metropolis criterion.
The *mu* keyword allows users to specify chemical potentials. This is
required and allowed only when using *semi-grand*\ . All chemical
@ -97,8 +96,8 @@ amount will have no effect on the simulation.
This command may optionally use the *region* keyword to define swap
volume. The specified region must have been previously defined with a
:doc:`region <region>` command. It must be defined with side = *in*\
. Swap attempts occur only between atoms that are both within the
:doc:`region <region>` command. It must be defined with side = *in*\ .
Swap attempts occur only between atoms that are both within the
specified region. Swaps are not otherwise attempted.
You should ensure you do not swap atoms belonging to a molecule, or
@ -147,7 +146,7 @@ Restart, fix_modify, output, run start/stop, minimize info
This fix writes the state of the fix to :doc:`binary restart files
<restart>`. This includes information about the random number
generator seed, the next timestep for MC exchanges, the number of
exchange attempts and successes etc. See the :doc:`read_restart
exchange attempts and successes, etc. See the :doc:`read_restart
<read_restart>` command for info on how to re-specify a fix in an
input script that reads a restart file, so that the operation of the
fix continues in an uninterrupted fashion.
@ -168,7 +167,7 @@ the following global cumulative quantities:
* 1 = swap attempts
* 2 = swap accepts
The vector values calculated by this fix are "extensive".
The vector values calculated by this fix are "extensive."
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during

99
doc/src/fix_ave_atom.rst
View File

@ -6,7 +6,7 @@ fix ave/atom command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ...
@ -41,7 +41,9 @@ Description
Use one or more per-atom vectors as inputs every few timesteps, and
average them atom by atom over longer timescales. The resulting
per-atom averages can be used by other :doc:`output commands <Howto_output>` such as the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` commands.
per-atom averages can be used by other :doc:`output commands <Howto_output>`
such as the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>`
commands.
The group specified with the command means only atoms within the group
have their averages computed. Results are set to 0.0 for atoms not in
@ -53,7 +55,8 @@ component) or can be the result of a :doc:`compute <compute>` or
:doc:`variable <variable>`. In the latter cases, the compute, fix, or
variable must produce a per-atom vector, not a global quantity or
local quantity. If you wish to time-average global quantities from a
compute, fix, or variable, then see the :doc:`fix ave/time <fix_ave_time>` command.
compute, fix, or variable, then see the :doc:`fix ave/time <fix_ave_time>`
command.
Each per-atom value of each input vector is averaged independently.
@ -66,18 +69,18 @@ per-atom vectors.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*" or
"m\*n". If N = the size of the vector (for *mode* = scalar) or the
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
"m\*n." If :math:`N` is the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
with no numeric values means all indices from 1 to :math:`N`. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
asterisk means all indices from m to :math:`N` (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/atom commands are
had been listed one by one. For example, these two fix ave/atom commands are
equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
command creates a per-atom array with 6 columns:
command creates a per-atom array with six columns:
.. code-block:: LAMMPS
@ -96,54 +99,58 @@ that are a multiple of *Nfreq*\ . The average is over *Nrepeat*
quantities, computed in the preceding portion of the simulation every
*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and
*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps
contributing to the average value cannot overlap,
i.e. Nrepeat\*Nevery can not exceed Nfreq.
contributing to the average value cannot overlap;
that is, :math:`N_\text{repeat} N_\text{every}` cannot exceed
:math:`N_\text{freq}`.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc.
For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
:math:`N_\text{freq}=100`, then values on timesteps 90, 92, 94, 96, 98, and 100
will be used to compute the final average on time step 100. Similarly for
timesteps 190, 192, 194, 196, 198, and 200 on time step 200, etc.
----------
The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
an input value from that compute.
The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, and
*fz*) are self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the
:doc:`compute property/atom <compute_property_atom>` command and then
specifying an input value from that compute.
.. note::
The x,y,z attributes are values that are re-wrapped inside the
periodic box whenever an atom crosses a periodic boundary. Thus if
you time average an atom that spends half its time on either side of
The *x*,*y*,*z* attributes are values that are re-wrapped inside the
periodic box whenever an atom crosses a periodic boundary. Thus, if
you time-average an atom that spends half of its time on either side of
the periodic box, you will get a value in the middle of the box. If
this is not what you want, consider averaging unwrapped coordinates,
which can be provided by the :doc:`compute property/atom <compute_property_atom>` command via its xu,yu,zu
attributes.
which can be provided by the
:doc:`compute property/atom <compute_property_atom>`
command via its *xu*, *yu*, and *zu* attributes.
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the compute is used. If a
bracketed term containing an index I is appended, the Ith column of
the per-atom array calculated by the compute is used. Users can also
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`. See the discussion above for how I can
bracketed term containing an index :math:`I` is appended, the
:math:`I^\text{th}` column of the per-atom array calculated by the compute is
used. Users can also write code for their own compute styles and
:doc:`add them to LAMMPS <Modify>`. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the fix is used. If a
bracketed term containing an index I is appended, the Ith column of
the per-atom array calculated by the fix is used. Note that some
fixes only produce their values on certain timesteps, which must be
compatible with *Nevery*, else an error will result. Users can also
write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`. See the discussion above for how I can be
specified with a wildcard asterisk to effectively specify multiple
values.
If a value begins with "f\_," a fix ID must follow which has been previously
defined in the input script. If no bracketed term is appended, the per-atom
vector calculated by the fix is used. If a bracketed term containing an index
:math:`I` is appended, the :math:`I^\text{th}` column of the per-atom array
calculated by the fix is used. Note that some fixes only produce their values
on certain timesteps, which must be compatible with *Nevery*, else an error
will result. Users can also write code for their own fix styles and
:doc:`add them to LAMMPS <Modify>`. See the discussion above for how I can be
specified with a wildcard asterisk to effectively specify multiple values.
If a value begins with "v\_", a variable name must follow which has
been previously defined in the input script as an :doc:`atom-style variable <variable>` Variables of style *atom* can reference
thermodynamic keywords, or invoke other computes, fixes, or variables
been previously defined in the input script as an
:doc:`atom-style variable <variable>`. Variables of style *atom* can reference
thermodynamic keywords or invoke other computes, fixes, or variables
when they are evaluated, so this is a very general means of generating
per-atom quantities to time average.
@ -152,9 +159,11 @@ per-atom quantities to time average.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global scalar or vector quantities are
stored by this fix for access by various :doc:`output commands <Howto_output>`.
No information about this fix is written to
:doc:`binary restart files <restart>`. None of the
:doc:`fix_modify <fix_modify>` options are relevant to this fix.
No global scalar or vector quantities are stored by this fix for access by
various :doc:`output commands <Howto_output>`.
This fix produces a per-atom vector or array which can be accessed by
various :doc:`output commands <Howto_output>`. A vector is produced if
@ -164,7 +173,8 @@ per-atom values can only be accessed on timesteps that are multiples
of *Nfreq* since that is when averaging is performed.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
@ -173,7 +183,8 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`compute <compute>`, :doc:`fix ave/histo <fix_ave_histo>`,
:doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`variable <variable>`,
Default

152
doc/src/fix_ave_chunk.rst
View File

@ -143,19 +143,19 @@ produce global quantities.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "\*" or "\*n" or "n\*" or
"m\*n". If N = the size of the vector (for *mode* = scalar) or the
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the
number of columns in the array (for *mode* = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
with no numeric values means all indices from 1 to :math:`N`. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
asterisk means all indices from m to :math:`N` (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/chunk commands are
had been listed one by one. For example, these two fix ave/chunk commands are
equivalent, since the :doc:`compute property/atom
<compute_property_atom>` command creates, in this case, a per-atom
array with 3 columns:
array with three columns:
.. code-block:: LAMMPS
@ -178,25 +178,26 @@ array with 3 columns:
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what
timesteps the input values will be accessed and contribute to the
average. The final averaged quantities are generated on timesteps
time steps the input values will be accessed and contribute to the
average. The final averaged quantities are generated on time steps
that are a multiples of *Nfreq*\ . The average is over *Nrepeat*
quantities, computed in the preceding portion of the simulation every
*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and
*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nrepeat\*Nevery
can not exceed Nfreq.
*Nevery* time steps. *Nfreq* must be a multiple of *Nevery* and
*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the time steps
contributing to the average value cannot overlap (i.e.,
:math:`N_\text{repeat}N_\text{every}` cannot exceed :math:`N_\text{freq}`).
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.
For example, if :math:`N_\text{every}=2`, :math:`N_\text{repeat}=6`, and
:math:`N_\text{freq}=100`, then values on
time steps 90, 92, 94, 96, 98, 100 will be used to compute the final average
on time step 100. Similarly for time steps 190, 192, 194, 196, 198, 200 on
time step 200, etc. If :math:`N_\text{repeat}=1` and
:math:`N_\text{freq} = 100`, then no time averaging is done; values are simply
generated on time steps 100, 200, etc.
Each input value can also be averaged over the atoms in each chunk.
The way the averaging is done across the *Nrepeat* timesteps to
produce output on the *Nfreq* timesteps, and across multiple *Nfreq*
The way the averaging is done across the *Nrepeat* time steps to
produce output on the *Nfreq* time steps, and across multiple *Nfreq*
outputs, is determined by the *norm* and *ave* keyword settings, as
discussed below.
@ -218,52 +219,53 @@ discussed below.
window, which can affect which atoms are discarded if the
simulation box size changes. If its *units* keyword is set to
*reduced*, then the number of bins *Nchunk* will still be fixed,
but the size of each bin can vary at each timestep if the
simulation box size changes, e.g. for an NPT simulation.
but the size of each bin can vary at each time step if the
simulation box size changes (e.g., for an NPT simulation).
----------
The atom attribute values (vx,vy,vz,fx,fy,fz,mass) are
The atom attribute values (*vx*, *vy*, *vz*, *fx*, *fy*, *fz*, *mass*) are
self-explanatory. As noted above, any other atom attributes can be
used as input values to this fix by using the :doc:`compute
property/atom <compute_property_atom>` command and then specifying an
input value from that compute.
The *density/number* value means the number density is computed for
each chunk, i.e. number/volume. The *density/mass* value means the
mass density is computed for each chunk, i.e. total-mass/volume. The
output values are in units of 1/volume or density (mass/volume). See
each chunk (i.e., number/volume). The *density/mass* value means the
mass density is computed for each chunk (i.e., total-mass/volume). The
output values are in units of 1/volume or mass density (mass/volume). See
the :doc:`units <units>` command page for the definition of density
for each choice of units, e.g. gram/cm\^3. If the chunks defined by
for each choice of units (e.g., g/cm\ :math:`^3`). If the chunks defined by
the :doc:`compute chunk/atom <compute_chunk_atom>` command are spatial
bins, the volume is the bin volume. Otherwise it is the volume of the
bins, the volume is the bin volume. Otherwise, it is the volume of the
entire simulation box.
The *temp* value means the temperature is computed for each chunk, by
the formula
The *temp* value means the temperature is computed for each chunk,
by the formula
.. math::
\text{KE} = \frac{\text{DOF}}{2} k_B T,
where KE = total kinetic energy of the chunk of atoms (sum of
:math:`\frac{1}{2} m v^2`), DOF = the total number of degrees of freedom
for all atoms in the chunk, :math:`k_B` = Boltzmann constant, and
:math:`T` = temperature.
where KE is the total kinetic energy of the chunk of atoms (sum of
:math:`\frac{1}{2} m v^2`), DOF is the the total number of degrees of freedom
for all atoms in the chunk, :math:`k_B` is the Boltzmann constant, and
:math:`T` is the absolute temperature.
The DOF is calculated as N\*adof + cdof, where N = number of atoms in
the chunk, adof = degrees of freedom per atom, and cdof = degrees of
freedom per chunk. By default adof = 2 or 3 = dimensionality of
system, as set via the :doc:`dimension <dimension>` command, and cdof =
0.0. This gives the usual formula for temperature.
The DOF is calculated as :math:`N`\ \*adof + cdof, where :math:`N` is the
number of atoms in the chunk, adof is the number of degrees of freedom per
atom, and cdof is the number of degrees of freedom per chunk. By default,
adof = 2 or 3 = dimensionality of system,
as set via the :doc:`dimension <dimension>` command, and cdof = 0.0.
This gives the usual formula for temperature.
Note that currently this temperature only includes translational
degrees of freedom for each atom. No rotational degrees of freedom
are included for finite-size particles. Also no degrees of freedom
are included for finite-size particles. Also, no degrees of freedom
are subtracted for any velocity bias or constraints that are applied,
such as :doc:`compute temp/partial <compute_temp_partial>`, or
:doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`. This is
because those degrees of freedom (e.g. a constrained bond) could apply
such as :doc:`compute temp/partial <compute_temp_partial>`,
:doc:`fix shake <fix_shake>`, or :doc:`fix rigid <fix_rigid>`. This is
because those degrees of freedom (e.g., a constrained bond) could apply
to sets of atoms that are both included and excluded from a specific
chunk, and hence the concept is somewhat ill-defined. In some cases,
you can use the *adof* and *cdof* keywords to adjust the calculated
@ -279,7 +281,7 @@ Note that the per-chunk temperature calculated by this fix and the
different. The compute calculates the temperature for each chunk for
a single snapshot. This fix can do that but can also time average
those values over many snapshots, or it can compute a temperature as
if the atoms in the chunk on different timesteps were collected
if the atoms in the chunk on different time steps were collected
together as one set of atoms to calculate their temperature. The
compute allows the center-of-mass velocity of each chunk to be
subtracted before calculating the temperature; this fix does not.
@ -289,8 +291,8 @@ previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the compute is used. Users can also write code for
their own compute styles and :doc:`add them to LAMMPS <Modify>`. See
the discussion above for how I can be specified with a wildcard
their own compute styles and :doc:`add them to LAMMPS <Modify>`.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
If a value begins with "f\_", a fix ID must follow which has been
@ -298,7 +300,7 @@ previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
their values on certain time steps, which must be compatible with
*Nevery*, else an error results. Users can also write code for their
own fix styles and :doc:`add them to LAMMPS <Modify>`. See the
discussion above for how I can be specified with a wildcard asterisk
@ -317,16 +319,16 @@ Additional optional keywords also affect the operation of this fix
and its outputs.
The *norm* keyword affects how averaging is done for the per-chunk
values that are output every *Nfreq* timesteps.
values that are output every *Nfreq* time steps.
It the *norm* setting is *all*, which is the default, a chunk value is
summed over all atoms in all *Nrepeat* samples, as is the count of
atoms in the chunk. The averaged output value for the chunk on the
*Nfreq* timesteps is Total-sum / Total-count. In other words it is an
*Nfreq* time steps is Total-sum / Total-count. In other words it is an
average over atoms across the entire *Nfreq* timescale. For the
*density/number* and *density/mass* values, the volume (bin volume or
system volume) used in the final normalization will be the volume at
the final *Nfreq* timestep. For the *temp* values, degrees of freedom
the final *Nfreq* time step. For the *temp* values, degrees of freedom
and kinetic energy are summed separately across the entire *Nfreq*
timescale, and the output value is calculated by dividing those two
sums.
@ -334,9 +336,9 @@ sums.
If the *norm* setting is *sample*, the chunk value is summed over
atoms for each sample, as is the count, and an "average sample value"
is computed for each sample, i.e. Sample-sum / Sample-count. The
output value for the chunk on the *Nfreq* timesteps is the average of
the *Nrepeat* "average sample values", i.e. the sum of *Nrepeat*
"average sample values" divided by *Nrepeat*\ . In other words it is an
output value for the chunk on the *Nfreq* time steps is the average of
the *Nrepeat* "average sample values" (i.e., the sum of *Nrepeat*
"average sample values" divided by *Nrepeat*\ ). In other words, it is an
average of an average. For the *density/number* and *density/mass*
values, the volume (bin volume or system volume) used in the
per-sample normalization will be the current volume at each sampling
@ -348,8 +350,8 @@ values" are "summed sample values". A summed sample value is simply
the chunk value summed over atoms in the sample, without dividing by
the number of atoms in the sample. The output value for the chunk on
the *Nfreq* timesteps is the average of the *Nrepeat* "summed sample
values", i.e. the sum of *Nrepeat* "summed sample values" divided by
*Nrepeat*\ . For the *density/number* and *density/mass* values, the
values" (i.e., the sum of *Nrepeat* "summed sample values" divided by
*Nrepeat*\ ). For the *density/number* and *density/mass* values, the
volume (bin volume or system volume) used in the per-sample sum
normalization will be the current volume at each sampling step.
@ -360,8 +362,7 @@ command or written to a file.
If the *ave* setting is *one*, which is the default, then the chunk
values produced on timesteps that are multiples of *Nfreq* are
independent of each other; they are output as-is without further
averaging.
independent of each other; they are output as-is without further averaging.
If the *ave* setting is *running*, then the chunk values produced on
timesteps that are multiples of *Nfreq* are summed and averaged in a
@ -369,48 +370,49 @@ cumulative sense before being output. Each output chunk value is thus
the average of the chunk value produced on that timestep with all
preceding values for the same chunk. This running average begins when
the fix is defined; it can only be restarted by deleting the fix via
the :doc:`unfix <unfix>` command, or re-defining the fix by
re-specifying it.
the :doc:`unfix <unfix>` command, or re-defining the fix by re-specifying it.
If the *ave* setting is *window*, then the chunk values produced on
timesteps that are multiples of *Nfreq* are summed and averaged within
a moving "window" of time, so that the last M values for the same
chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
then the output on step 10000 will be the average of the individual
chunk values on steps 8000,9000,10000. Outputs on early steps will
average over less than M values if they are not available.
a moving "window" of time, so that the last :math:`M` values for the same
chunk are used to produce the output. For example, if :math:`M = 3` and
:math:`N_\text{freq} = 1000`, then the output on step 10000 will be the average
of the individual chunk values on steps 8000,9000,10000. Outputs on early
steps will average over less than :math:`M` values if they are not available.
The *bias* keyword specifies the ID of a temperature compute that
removes a "bias" velocity from each atom, specified as *bias-ID*\ . It
is only used when the *temp* value is calculated, to compute the
removes a "bias" velocity from each atom, specified as *bias-ID*\ .
It is only used when the *temp* value is calculated, to compute the
thermal temperature of each chunk after the translational kinetic
energy components have been altered in a prescribed way, e.g. to
remove a flow velocity profile. See the doc pages for individual
computes that calculate a temperature to see which ones implement a
bias.
energy components have been altered in a prescribed way, (e.g., to
remove a flow velocity profile). See the doc pages for individual
computes that calculate a temperature to see which ones implement a bias.
The *adof* and *cdof* keywords define the values used in the degree of
freedom (DOF) formula described above for temperature calculation
for each chunk. They are only used when the *temp* value is
calculated. They can be used to calculate a more appropriate
temperature for some kinds of chunks. Here are 3 examples:
temperature for some kinds of chunks. Here are three examples:
If spatially binned chunks contain some number of water molecules and
:doc:`fix shake <fix_shake>` is used to make each molecule rigid, then
you could calculate a temperature with 6 degrees of freedom (DOF) (3
translational, 3 rotational) per molecule by setting *adof* to 2.0.
you could calculate a temperature with 6 degrees of freedom (DOF) (three
translational, three rotational) per molecule by setting *adof* to 2.0.
If :doc:`compute temp/partial <compute_temp_partial>` is used with the
*bias* keyword to only allow the x component of velocity to contribute
*bias* keyword to only allow the :math:`x` component of velocity to contribute
to the temperature, then *adof* = 1.0 would be appropriate.
If each chunk consists of a large molecule, with some number of its
bonds constrained by :doc:`fix shake <fix_shake>` or the entire molecule
by :doc:`fix rigid/small <fix_rigid>`, *adof* = 0.0 and *cdof* could be
set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
(entire chunk in this case), that is, 6 for 3d or 3 for 2d for a rigid
molecule.
..
FIXME need to make *Nfreq* vs. :math:`N_\text{freq}` consistent.
The *file* keyword allows a filename to be specified. Every *Nfreq*
timesteps, a section of chunk info will be written to a text file in
the following format. A line with the timestep and number of chunks